Gaps: Editing symbols that are inserted into sequences in the
process of alignment in order to compensate for presumptive insertion
and deletion events.

Gel electrophoresis: A technique used to detect differences
in proteins and polypeptide chains based on differences in the size
and electrical charges of the molecules.

Gene flow: Genetic exchange between populations resulting from
the dispersal of gametes, zygotes or individuals.

Genome: The entire complement of genetic material in a cell.

Genotype: The genetic make-up of an individual in respect of
one genetic locus, a group of loci or even its total genetic complement.

Homology: Common ancestry of two or more genes or gene products.

Homoplasy: A collection of phenomena that leads to similarities
in character states for reasons other than inheritance from a common
ancestor.

Ingroup: An assumed monophyletic group, usually comprising
the taxa of primary interest.

Jackknifing: A statistical method of numerical resampling based
on deleting a portion of the original observations in subsequent samples.

Maximum likelihood: A method of determining which of two or
more competing hypotheses (such as alternative phylogenetic trees) yields
best fits to the data.

Maximum parsimony: A criterion for estimating a parameter from
observed data based on the principle of minimising the number of events
needed to explain the data. In phylogenetic analysis, the optimal tree
under the maximum parsimony criterion is the tree that requires the
fewest number of character-state changes.

Molecular clock: A theoretical clock based on the assumption
that the rates at which nucleotide (or amino acid) substitutions become
fixed in evolutionary lineages is approximately constant for a given
DNA sequence (or polypeptide chain) and reflects the time since data
diverged.

Molecular systematics: The detection, description, and explanation
of molecular biological diversity, both within and among species.

Monophyletic: A group of taxa that contains an ancestor and
all of its descendants.

Mutation: Any change which alters the identity or order of
nucleotide bases within a chromosome.

Natural selection: According to Charles Darwin, the main mechanism
giving rise to evolution. The mechanism by which heritable traits which
increase an organism's chances of survival and reproduction are more
likely to be passed on to the next generation than less advantageous
traits.

Nucleotide base: The structural unit of a nucleic acid. The
major nucleotide bases in DNA are the purines adenine and guanine, and
the pyrimidines cytosine and thymine, of which the latter is replaced
by uracil in RNA.